library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
## 2(3):100141
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:clusterProfiler':
## 
##     rename
## The following object is masked from 'package:utils':
## 
##     findMatches
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:clusterProfiler':
## 
##     slice
## The following object is masked from 'package:grDevices':
## 
##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
## 
##     select
## 
library(stringr)
library(ggplot2)

The results here are deprecated in favor of lambda.1se Cox Glmnet.

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.glmnet.cox = readRDS("data/sel_features/results_glmnet_cox_coef.rds")
sel.features = results.glmnet.cox
sel.features
## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$dev
##  hsa-mir-101-2   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b 
##   -0.350155993   -0.214528093   -0.992011646    0.772882470    0.102110997 
## hsa-mir-199a-1 hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c hsa-mir-3199-1 
##    0.111474373    0.306494391    0.409242447   -0.164814191   -0.188845820 
## hsa-mir-320c-2    hsa-mir-375   hsa-mir-3912   hsa-mir-3923 hsa-mir-513a-2 
##   -0.443119925    0.066404104   -0.008097655    0.190177197   -0.024029228 
##   hsa-mir-513b    hsa-mir-605    hsa-mir-625    hsa-mir-659    hsa-mir-664 
##   -0.020939139   -0.120147454   -0.098469616   -0.182484891   -0.799992602 
##    hsa-mir-7-1    hsa-mir-874    MRE11A.R2Gn      AKT1.R2Gn     RAD51.R2Gn 
##    1.148233824   -0.137903989    0.389314476   -0.159434639    0.845634933 
##     MAPK9.R2Gn     MAPK3.R2Gn     STMN1.R2Gn     CHEK1.R2Gn     ACACA.R2Gn 
##   -0.188024741   -0.742060120    0.008038958    0.767719561    0.174201855 
##     WWTR1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn    BCL2L1.R2Gn      TYMS.R2Gn 
##    0.136573360    0.161836438   -0.497987521   -0.069660519    0.302743158 
##     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA 
##    0.577031225   -1.626099874   -0.090385350    0.447771957    0.120146812 
##        CLDN7.g         LCN2.g        PTCH1.g        ANXA1.g          SYK.g 
##   -0.176602768    0.017903924    0.017683893    0.338981167    0.017503331 
## 
## $fold3$elasticnet_0.5$c
##  hsa-mir-101-2   hsa-mir-106b   hsa-mir-1248   hsa-mir-125a  hsa-mir-1274b 
##  -1.1694665475   0.9939393131   0.0672855648  -0.0880316837   0.0413862603 
##   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b    hsa-mir-141 hsa-mir-199a-1 
##  -2.1470224865   2.4683436568   0.3610700379   0.0553130529   0.4249486572 
## hsa-mir-199a-2   hsa-mir-199b    hsa-mir-205    hsa-mir-214  hsa-mir-29b-2 
##   0.6303162842   0.7774098133  -0.2308378206   0.2173213142  -0.0496921973 
##    hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2    hsa-mir-330    hsa-mir-34a 
##  -0.5710787182  -0.3552181895  -0.8289791394   0.6217391706  -0.4020065803 
##   hsa-mir-3682    hsa-mir-375   hsa-mir-3912   hsa-mir-3923 hsa-mir-3926-2 
##   0.3216882596   0.5288068992  -0.8446616535   0.4345049389  -0.3558452034 
## hsa-mir-513a-2   hsa-mir-513b    hsa-mir-585    hsa-mir-605    hsa-mir-618 
##  -0.1193808139  -0.1813210601  -0.0562017121  -0.1091441112   0.0143143416 
##    hsa-mir-625    hsa-mir-659    hsa-mir-664    hsa-mir-670    hsa-mir-7-1 
##  -0.3807221774  -0.4441593672  -1.1888078114  -0.0222466593   2.5098621174 
##    hsa-mir-874    hsa-mir-942     hsa-mir-98     PRKCD.R2Gn    MRE11A.R2Gn 
##  -0.7490715485   0.7935448724  -0.0186144163  -0.1722509236   0.9919023793 
##   BCL2L11.R2Gn      AKT1.R2Gn     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn 
##  -1.1441582713  -0.2532545544   1.9596943782  -0.7722498402  -1.5255831798 
##      TSC2.R2Gn      ANLN.R2Gn     STMN1.R2Gn     CHEK1.R2Gn     ACACA.R2Gn 
##  -0.9241345286   0.1201372547   0.2872013887   0.8235879048   0.6425941521 
##     WWTR1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn    BCL2L1.R2Gn      TYMS.R2Gn 
##   0.6090214863   0.5051537025  -1.0936388403  -0.3779508474   0.9823122125 
##    PRKAA1.R2Gn     FOXM1.R2Gn      XIAP.R2Gn      TFRC.R2Gn     PREX1.R2Gn 
##  -0.0737130824   0.9429754576  -3.0339719950   0.0280523460  -0.2536857447 
##       RET.R2Gn    INPP4B.RPPA      TFRC.RPPA       MRE11A.M        PRDX1.M 
##   1.6495446315  -0.0020651078   0.2151841797   0.6657256474   0.6609214928 
##        CASP8.M        CLDN7.g        YWHAE.g         LCN2.g        PRKCA.g 
##   0.6565872959  -0.7049847863  -0.0001312615   0.4015385931  -0.0043660472 
##        PTCH1.g        ANXA1.g          SYK.g 
##   0.3456107175   0.6449071241   0.3445385423 
## 
## 
## $fold3$lasso
## $fold3$lasso$dev
##   hsa-mir-1277   hsa-mir-199b hsa-mir-320c-2   hsa-mir-3923    hsa-mir-605 
##     -0.4394996      0.3837893     -0.5630734      0.2036978     -0.2603078 
##    hsa-mir-664    hsa-mir-7-1     MAPK3.R2Gn     CHEK1.R2Gn     FOXM1.R2Gn 
##     -0.5998023      1.4806307     -0.7712527      0.1470129      1.2302967 
##      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA        ANXA1.g 
##     -3.2083424     -0.1273675      0.2230730      0.1582401      0.3253384 
## 
## $fold3$lasso$c
##   hsa-mir-199b hsa-mir-320c-2   hsa-mir-3923    hsa-mir-605    hsa-mir-664 
##     0.05513951    -0.20961965     0.11298397    -0.02772348    -1.55408650 
##    hsa-mir-7-1     MAPK3.R2Gn     FOXM1.R2Gn      XIAP.R2Gn      TFRC.RPPA 
##     0.43950110    -0.61489862     1.18618843    -1.63439254     0.08341764 
##        ANXA1.g 
##     0.01920368 
## 
## 
## 
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$dev
##  hsa-mir-101-2   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b 
##  -0.2487331002  -0.2138861754  -0.7237625743   0.5319734262   0.0962757577 
## hsa-mir-199a-1 hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c hsa-mir-3199-1 
##   0.0305729960   0.2274006887   0.3316056764  -0.1219358392  -0.1370852349 
## hsa-mir-320c-2   hsa-mir-3923 hsa-mir-513a-2   hsa-mir-513b    hsa-mir-605 
##  -0.3568352118   0.1713901420  -0.0009106425  -0.0280204290  -0.1043171173 
##    hsa-mir-659    hsa-mir-664    hsa-mir-7-1    hsa-mir-874    MRE11A.R2Gn 
##  -0.0213122856  -0.8787615701   0.8237097189  -0.0457758136   0.2093189696 
##      AKT1.R2Gn     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn     STMN1.R2Gn 
##  -0.0821184996   0.6485341074  -0.1381725768  -0.6903401762   0.0094342060 
##     CHEK1.R2Gn     ACACA.R2Gn     WWTR1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn 
##   0.7224003758   0.0930371590   0.0280686906   0.1643475351  -0.4101522402 
##    BCL2L1.R2Gn      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn 
##  -0.0111451156   0.1984583172   0.5764641758  -1.4422087427  -0.0990588693 
##       RET.R2Gn      TFRC.RPPA        CLDN7.g        ANXA1.g 
##   0.2341015550   0.0989335121  -0.0902252283   0.2727080779 
## 
## $fold5$elasticnet_0.5$c
##  hsa-mir-101-1  hsa-mir-101-2   hsa-mir-106b   hsa-mir-1248   hsa-mir-125a 
##   -0.201308360   -1.773219117    1.976720264    0.086115803   -0.261421179 
##  hsa-mir-1274b   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b   hsa-mir-135b 
##    0.202062481   -2.692688527    3.354246674    0.758584236    0.028233851 
##    hsa-mir-141    hsa-mir-182    hsa-mir-183 hsa-mir-199a-1 hsa-mir-199a-2 
##    0.231196842    0.157599528    0.080580175    0.613351302    0.821912752 
##   hsa-mir-199b   hsa-mir-200c    hsa-mir-205    hsa-mir-214  hsa-mir-218-2 
##    0.994060971    0.021174050   -0.338170725    0.482140928    0.233180872 
##   hsa-mir-24-2  hsa-mir-29b-1  hsa-mir-29b-2    hsa-mir-29c hsa-mir-3199-1 
##    0.283680849   -0.002391981   -0.289665106   -0.895073393   -0.439936080 
## hsa-mir-320c-2    hsa-mir-330    hsa-mir-34a    hsa-mir-34b   hsa-mir-3651 
##   -1.044015317    0.826943948   -0.589169348   -0.110954508    0.132388904 
##   hsa-mir-3682    hsa-mir-375   hsa-mir-378c   hsa-mir-3912   hsa-mir-3923 
##    0.651063342    0.623843699   -0.037982216   -1.343478336    0.567109871 
## hsa-mir-3926-2    hsa-mir-506 hsa-mir-513a-2   hsa-mir-513b  hsa-mir-514-1 
##   -0.518159096   -0.096647517   -0.209765225   -0.323526454   -0.118733228 
##  hsa-mir-514-2  hsa-mir-514-3    hsa-mir-585    hsa-mir-605    hsa-mir-618 
##   -0.047805602   -0.103089491   -0.155063543   -0.084879510    0.251193194 
##    hsa-mir-625    hsa-mir-639    hsa-mir-659    hsa-mir-664    hsa-mir-670 
##   -0.570359326    0.066322151   -0.421888900   -1.565739054   -0.252330829 
##    hsa-mir-675    hsa-mir-7-1    hsa-mir-874    hsa-mir-935    hsa-mir-942 
##    0.081285594    3.049883209   -1.053395300    0.030234096    1.448856059 
##     hsa-mir-98     PRKCD.R2Gn    MRE11A.R2Gn   BCL2L11.R2Gn      AKT1.R2Gn 
##   -0.430520066   -0.509651360    1.565059709   -2.432203359   -0.274855383 
##     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn      TSC2.R2Gn      YBX1.R2Gn 
##    2.806088205   -1.181946610   -1.955540830   -1.670483259    0.171588972 
##      ANLN.R2Gn     STMN1.R2Gn     CHEK1.R2Gn     ACACA.R2Gn     WWTR1.R2Gn 
##    0.334199263    0.484933216    1.174045018    1.013673285    1.020686914 
##      CDK1.R2Gn     EEF2K.R2Gn      E2F1.R2Gn    BCL2L1.R2Gn      TYMS.R2Gn 
##    0.753225907   -1.429715064    0.125645209   -0.485993782    1.483321848 
##     CCNB1.R2Gn    PRKAA1.R2Gn     FOXM1.R2Gn      XIAP.R2Gn      EZH2.R2Gn 
##    0.141516835   -0.253035531    1.294900486   -3.909023944    0.038030836 
##      TFRC.R2Gn     PREX1.R2Gn       RET.R2Gn     RBM15.RPPA      FASN.RPPA 
##    0.090703812   -0.362755183    2.247752934    0.001166909    0.007560847 
##    INPP4B.RPPA     PRDX1.RPPA      XBP1.RPPA     MYH11.RPPA      TFRC.RPPA 
##   -0.086372376   -0.023970279   -0.003008107   -0.032501540    0.275985560 
##       MRE11A.M        PRDX1.M        CASP8.M      RPS6KA1.g        CLDN7.g 
##    0.910710965    0.900001325    0.892586976   -0.008094269   -0.963983420 
##        YWHAE.g         TSC1.g         LCN2.g         YBX1.g        PRKCA.g 
##   -0.253692611    0.016487783    0.685000188   -0.015758124   -0.206429629 
##         TTF1.g        STMN1.g          LCK.g        PTCH1.g         NRG1.g 
##    0.015023530   -0.005567201   -0.014720701    0.563989120   -0.013630544 
##        ANXA1.g       ARID1A.g        CASP9.g          SYK.g 
##    0.789714277   -0.005287740   -0.049204012    0.561479894 
## 
## 
## $fold5$lasso
## $fold5$lasso$dev
##   hsa-mir-1277   hsa-mir-199b hsa-mir-320c-2   hsa-mir-3923    hsa-mir-605 
##    -0.67773818     0.62816836    -0.83120225     0.30885307    -0.40239153 
##    hsa-mir-7-1     MAPK3.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn 
##     2.30548432    -0.93163045     1.27399975    -4.55339637    -0.31389159 
##       RET.R2Gn      TFRC.RPPA        CLDN7.g        ANXA1.g 
##     0.92385933     0.23700126    -0.07317507     0.47557184 
## 
## $fold5$lasso$c
##   hsa-mir-1277   hsa-mir-1307   hsa-mir-199b    hsa-mir-206 hsa-mir-3199-1 
##   -8.599721014    2.381186070    0.757142663    0.578828208   -0.019996140 
## hsa-mir-320c-2    hsa-mir-34b   hsa-mir-3912   hsa-mir-3923    hsa-mir-605 
##   -3.506592441   -0.005931603   -1.778975918    1.717924552   -0.292410032 
##    hsa-mir-659    hsa-mir-7-1     PRKCD.R2Gn      TGM2.R2Gn     EEF2K.R2Gn 
##   -0.687612334   10.532592779   -0.964084574   -0.095915019   -0.002119239 
##      TYMS.R2Gn      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA 
##    5.861599651  -14.760541137   -1.054684473    4.288179571    0.977957115 
##        CLDN7.g         LCN2.g        ANXA1.g 
##   -0.980562035    0.007399925    1.346039542 
## 
## 
## 
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$dev
##  hsa-mir-101-2   hsa-mir-1248   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307 
##   -0.380733378    0.005417786   -0.212753463   -1.097413125    0.890227464 
##   hsa-mir-130b hsa-mir-199a-1 hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c 
##    0.106661442    0.147070108    0.340762226    0.444364704   -0.183946171 
## hsa-mir-3199-1 hsa-mir-320c-2    hsa-mir-330    hsa-mir-34a    hsa-mir-375 
##   -0.208247651   -0.481071547    0.022451088   -0.006020326    0.103285010 
##   hsa-mir-3912   hsa-mir-3923 hsa-mir-513a-2   hsa-mir-513b    hsa-mir-605 
##   -0.043485404    0.201580727   -0.032413924   -0.023723027   -0.121922078 
##    hsa-mir-625    hsa-mir-659    hsa-mir-664    hsa-mir-7-1    hsa-mir-874 
##   -0.157904055   -0.250608682   -0.769339432    1.314703922   -0.192661457 
##    MRE11A.R2Gn      AKT1.R2Gn     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn 
##    0.459972690   -0.190817233    0.932827503   -0.221266059   -0.793580783 
##     STMN1.R2Gn     CHEK1.R2Gn     ACACA.R2Gn     WWTR1.R2Gn      CDK1.R2Gn 
##    0.008947456    0.771942369    0.211037000    0.156130430    0.168859365 
##     EEF2K.R2Gn    BCL2L1.R2Gn      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn 
##   -0.545750898   -0.099504495    0.359293058    0.584257453   -1.713000369 
##     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA       MRE11A.M        PRDX1.M 
##   -0.080329221    0.551579545    0.128505126    0.020265007    0.019000912 
##        CASP8.M        CLDN7.g         LCN2.g        PTCH1.g        ANXA1.g 
##    0.017616576   -0.209202528    0.043701084    0.032915897    0.366740940 
##          SYK.g 
##    0.032538271 
## 
## $fold10$elasticnet_0.5$c
##  hsa-mir-101-2   hsa-mir-1248   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307 
##  -0.3743394226   0.0014064170  -0.2098131809  -1.0615988337   0.8538411932 
##   hsa-mir-130b hsa-mir-199a-1 hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c 
##   0.1008589375   0.1344075653   0.3283759475   0.4311534943  -0.1760670088 
## hsa-mir-3199-1 hsa-mir-320c-2    hsa-mir-330    hsa-mir-375   hsa-mir-3912 
##  -0.2035108945  -0.4684815177   0.0020100454   0.0943467281  -0.0268227969 
##   hsa-mir-3923 hsa-mir-513a-2   hsa-mir-513b    hsa-mir-605    hsa-mir-625 
##   0.1971808416  -0.0314791009  -0.0226278363  -0.1228908997  -0.1445423962 
##    hsa-mir-659    hsa-mir-664    hsa-mir-7-1    hsa-mir-874    MRE11A.R2Gn 
##  -0.2325442678  -0.7735961116   1.2614344211  -0.1745783158   0.4458196946 
##      AKT1.R2Gn     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn     STMN1.R2Gn 
##  -0.1831727360   0.9051518480  -0.2079256975  -0.7665676549   0.0081459419 
##     CHEK1.R2Gn     ACACA.R2Gn     WWTR1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn 
##   0.7786765864   0.1980764980   0.1633067630   0.1654077390  -0.5257128074 
##    BCL2L1.R2Gn      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn 
##  -0.0869265810   0.3401955911   0.5783857162  -1.6858835763  -0.0852994606 
##       RET.R2Gn      TFRC.RPPA       MRE11A.M        PRDX1.M        CASP8.M 
##   0.5149394140   0.1260665458   0.0036573052   0.0016799307   0.0005799475 
##        CLDN7.g         LCN2.g        PTCH1.g        ANXA1.g          SYK.g 
##  -0.2006189206   0.0346504587   0.0257076791   0.3573753984   0.0252179798 
## 
## 
## $fold10$lasso
## $fold10$lasso$dev
##   hsa-mir-1277   hsa-mir-199b hsa-mir-320c-2   hsa-mir-3923    hsa-mir-605 
##    -0.20697924     0.27101137    -0.45836489     0.16268941    -0.20086620 
##    hsa-mir-664    hsa-mir-7-1     MAPK3.R2Gn     FOXM1.R2Gn      XIAP.R2Gn 
##    -0.99585084     1.15564264    -0.71175862     1.25987310    -2.66585354 
##     PREX1.R2Gn      TFRC.RPPA        ANXA1.g 
##    -0.07326543     0.13317715     0.24514283 
## 
## $fold10$lasso$c
##   hsa-mir-1248   hsa-mir-1277   hsa-mir-199b hsa-mir-3199-1 hsa-mir-320c-2 
##    0.024224712   -1.278133246    0.864526911   -0.078510146   -1.174025346 
##   hsa-mir-3912   hsa-mir-3923    hsa-mir-605    hsa-mir-659    hsa-mir-7-1 
##   -0.275734483    0.410449853   -0.468817660   -0.153424440    3.402876154 
##      AKT1.R2Gn     MAPK3.R2Gn     WWTR1.R2Gn    RAB11B.R2Gn      TYMS.R2Gn 
##   -0.005319532   -0.761099817    0.007425546   -0.210285468    0.175029702 
##     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA 
##    1.324306495   -5.948007671   -0.478619972    1.537704089    0.333768394 
##        CLDN7.g        ANXA1.g 
##   -0.135997589    0.640172045

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  #Mutations and gistict for glmnet only
  out.M = variable.list[endsWith(variable.list, ".M")] 
  out.g = variable.list[endsWith(variable.list, ".g")] 
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA,
             "Mutations" = out.M,
             "gistict" = out.g)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  M.genes = str_remove(multiomics.list[[4]], ".M")
  
  g.genes = str_remove(multiomics.list[[5]], ".g")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
  out = as.character(unique(out1))
  out
}

Some microRNAs are dropped as they do not contribute enough to convert to genes.

geneNames <- list("3F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$dev)),
                  "3F_0.5_C" = multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$c)),
                  "3F_1_DEV" = multiomics.to.GENES(names(sel.features$fold3$lasso$dev), drop.miRNA = T),
                  "3F_1_C" = multiomics.to.GENES(names(sel.features$fold3$lasso$c), drop.miRNA = T),
                  "5F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$dev), drop.miRNA = T), 
                  "5F_0.5_C" = multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$c)),
                  "5F_1_DEV" = multiomics.to.GENES(names(sel.features$fold5$lasso$dev), drop.miRNA = T),
                  "5F_1_C" = multiomics.to.GENES(names(sel.features$fold5$lasso$c)),
                  "10F_0.5_DEV" = multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$dev)),
                  "10F_0.5_C" = multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$c)),
                  "10F_1_DEV" = multiomics.to.GENES(names(sel.features$fold10$lasso$dev), drop.miRNA = T),
                  "10F_1_C" = multiomics.to.GENES(names(sel.features$fold10$lasso$c))
                  )
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
geneNames
## $`3F_0.5_DEV`
##  [1] "BCL2"    "ERBB2"   "AXL"     "BAK1"    "MYC"     "CASP3"   "BCL2L11"
##  [8] "TP53"    "YAP1"    "YWHAZ"   "STAT3"   "PARP1"   "XIAP"    "CTNNB1" 
## [15] "IGF1R"   "PRDX1"   "PDK1"    "PIK3CA"  "PRKCA"   "MAPK3"   "TFRC"   
## [22] "TGM2"    "MYH9"    "CDKN1A"  "IRS1"    "JUN"     "RAF1"    "TYMS"   
## [29] "FOXO3"   "ANXA7"   "CLDN7"   "CTNNA1"  "EIF4G1"  "YBX1"    "RPS6"   
## [36] "SRSF1"   "NDRG1"   "PECAM1"  "YWHAB"   "SETD2"   "MRE11A"  "AKT1"   
## [43] "RAD51"   "MAPK9"   "STMN1"   "CHEK1"   "ACACA"   "WWTR1"   "CDK1"   
## [50] "EEF2K"   "BCL2L1"  "FOXM1"   "PREX1"   "RET"     "LCN2"    "PTCH1"  
## [57] "ANXA1"   "SYK"    
## 
## $`3F_0.5_C`
##  [1] "CDKN1A"  "MYC"     "VHL"     "STAT3"   "DVL3"    "BCL2"    "ERBB2"  
##  [8] "AXL"     "BAK1"    "CASP3"   "BCL2L11" "TP53"    "YAP1"    "YWHAZ"  
## [15] "PARP1"   "XIAP"    "CTNNB1"  "IGF1R"   "PRDX1"   "PDK1"    "PIK3CA" 
## [22] "PRKCA"   "MAPK3"   "TFRC"    "TGM2"    "NCOA3"   "MYH9"    "IRS1"   
## [29] "JUN"     "EZH2"    "RAF1"    "TYMS"    "FOXO3"   "ANXA7"   "CLDN7"  
## [36] "CTNNA1"  "EIF4G1"  "YBX1"    "MAPK8"   "RPS6"    "SRSF1"   "NDRG1"  
## [43] "ANLN"    "PECAM1"  "ERCC1"   "YWHAB"   "SETD2"   "PRKCD"   "MRE11A" 
## [50] "AKT1"    "RAD51"   "MAPK9"   "TSC2"    "STMN1"   "CHEK1"   "ACACA"  
## [57] "WWTR1"   "CDK1"    "EEF2K"   "BCL2L1"  "PRKAA1"  "FOXM1"   "PREX1"  
## [64] "RET"     "INPP4B"  "CASP8"   "YWHAE"   "LCN2"    "PTCH1"   "ANXA1"  
## [71] "SYK"    
## 
## $`3F_1_DEV`
## [1] "MAPK3" "CHEK1" "FOXM1" "XIAP"  "PREX1" "RET"   "TFRC"  "ANXA1"
## 
## $`3F_1_C`
## [1] "MAPK3" "FOXM1" "XIAP"  "TFRC"  "ANXA1"
## 
## $`5F_0.5_DEV`
##  [1] "MRE11A" "AKT1"   "RAD51"  "MAPK9"  "MAPK3"  "STMN1"  "CHEK1"  "ACACA" 
##  [9] "WWTR1"  "CDK1"   "EEF2K"  "BCL2L1" "TYMS"   "FOXM1"  "XIAP"   "PREX1" 
## [17] "RET"    "TFRC"   "CLDN7"  "ANXA1" 
## 
## $`5F_0.5_C`
##  [1] "CDKN1A"  "MYC"     "VHL"     "NOTCH1"  "XIAP"    "CDK1"    "YBX1"   
##  [8] "BECN1"   "STAT3"   "DVL3"    "PEA15"   "AKT1"    "ACACA"   "BCL2"   
## [15] "ERBB2"   "AXL"     "BAK1"    "CASP3"   "BCL2L11" "TP53"    "YAP1"   
## [22] "YWHAZ"   "PARP1"   "CTNNB1"  "IGF1R"   "PRDX1"   "PDK1"    "PIK3CA" 
## [29] "PRKCA"   "MAPK3"   "TFRC"    "TGM2"    "PTEN"    "NCOA3"   "MYH9"   
## [36] "IRS1"    "JUN"     "EZH2"    "RAF1"    "TYMS"    "FOXO3"   "BCL2L1" 
## [43] "ANXA7"   "CLDN7"   "CTNNA1"  "EEF2"    "EIF4G1"  "GATA3"   "GSK3B"  
## [50] "MSH6"    "NRG1"    "MAPK1"   "MAPK8"   "RPS6"    "SRSF1"   "TUBA1B" 
## [57] "NDRG1"   "ANLN"    "AKT1S1"  "RICTOR"  "PECAM1"  "ERCC1"   "TP53BP1"
## [64] "YWHAB"   "SETD2"   "GSK3A"   "PRKCD"   "MRE11A"  "RAD51"   "MAPK9"  
## [71] "TSC2"    "STMN1"   "CHEK1"   "WWTR1"   "EEF2K"   "E2F1"    "CCNB1"  
## [78] "PRKAA1"  "FOXM1"   "PREX1"   "RET"     "RBM15"   "FASN"    "INPP4B" 
## [85] "XBP1"    "MYH11"   "CASP8"   "RPS6KA1" "YWHAE"   "TSC1"    "LCN2"   
## [92] "TTF1"    "LCK"     "PTCH1"   "ANXA1"   "ARID1A"  "CASP9"   "SYK"    
## 
## $`5F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP"  "PREX1" "RET"   "TFRC"  "CLDN7" "ANXA1"
## 
## $`5F_1_C`
##  [1] "ESR1"   "MET"    "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3" "AKT1"  
##  [9] "IGF1R"  "FOXO3"  "CHEK1"  "FN1"    "PRKCD"  "TGM2"   "EEF2K"  "TYMS"  
## [17] "XIAP"   "PREX1"  "RET"    "TFRC"   "CLDN7"  "LCN2"   "ANXA1" 
## 
## $`10F_0.5_DEV`
##  [1] "CDKN1A"  "MYC"     "VHL"     "BCL2"    "ERBB2"   "AXL"     "BAK1"   
##  [8] "CASP3"   "BCL2L11" "TP53"    "YAP1"    "YWHAZ"   "STAT3"   "PARP1"  
## [15] "XIAP"    "CTNNB1"  "IGF1R"   "PRDX1"   "PDK1"    "PIK3CA"  "PRKCA"  
## [22] "MAPK3"   "TFRC"    "TGM2"    "MYH9"    "IRS1"    "JUN"     "RAF1"   
## [29] "TYMS"    "FOXO3"   "ANXA7"   "CLDN7"   "CTNNA1"  "EIF4G1"  "YBX1"   
## [36] "RPS6"    "SRSF1"   "NDRG1"   "PECAM1"  "YWHAB"   "SETD2"   "MRE11A" 
## [43] "AKT1"    "RAD51"   "MAPK9"   "STMN1"   "CHEK1"   "ACACA"   "WWTR1"  
## [50] "CDK1"    "EEF2K"   "BCL2L1"  "FOXM1"   "PREX1"   "RET"     "CASP8"  
## [57] "LCN2"    "PTCH1"   "ANXA1"   "SYK"    
## 
## $`10F_0.5_C`
##  [1] "CDKN1A"  "MYC"     "VHL"     "BCL2"    "ERBB2"   "AXL"     "BAK1"   
##  [8] "CASP3"   "BCL2L11" "TP53"    "YAP1"    "YWHAZ"   "STAT3"   "PARP1"  
## [15] "XIAP"    "CTNNB1"  "IGF1R"   "PRDX1"   "PDK1"    "PIK3CA"  "PRKCA"  
## [22] "MAPK3"   "TFRC"    "TGM2"    "MYH9"    "IRS1"    "JUN"     "RAF1"   
## [29] "TYMS"    "FOXO3"   "ANXA7"   "CLDN7"   "CTNNA1"  "EIF4G1"  "YBX1"   
## [36] "RPS6"    "SRSF1"   "NDRG1"   "PECAM1"  "YWHAB"   "SETD2"   "MRE11A" 
## [43] "AKT1"    "RAD51"   "MAPK9"   "STMN1"   "CHEK1"   "ACACA"   "WWTR1"  
## [50] "CDK1"    "EEF2K"   "BCL2L1"  "FOXM1"   "PREX1"   "RET"     "CASP8"  
## [57] "LCN2"    "PTCH1"   "ANXA1"   "SYK"    
## 
## $`10F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP"  "PREX1" "TFRC"  "ANXA1"
## 
## $`10F_1_C`
##  [1] "CDKN1A" "MYC"    "VHL"    "AKT1"   "MAPK3"  "WWTR1"  "RAB11B" "TYMS"  
##  [9] "FOXM1"  "XIAP"   "PREX1"  "RET"    "TFRC"   "CLDN7"  "ANXA1"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet_cox_min.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/58
## GO:0003824 GO:0003824           catalytic activity    25     25/58
## GO:0005198 GO:0005198 structural molecule activity     3      3/58
## GO:0005215 GO:0005215         transporter activity     3      3/58
## GO:0005488 GO:0005488                      binding    57     57/58
## GO:0009055 GO:0009055   electron transfer activity     0      0/58
##                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                MYH9
## GO:0003824                                                                                                                                                                                          ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CDKN1A/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/SYK
## GO:0005198                                                                                                                                                                                                                                                                                                                   CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                     BCL2/BAK1/IGF1R
## GO:0005488 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0009055                                                                                                                                                                                                                                                                                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    18     18/58
## GO:0002376 GO:0002376 immune system process    33     33/58
## GO:0008152 GO:0008152     metabolic process    51     51/58
## GO:0009987 GO:0009987      cellular process    57     57/58
## GO:0016032 GO:0016032         viral process     7      7/58
## GO:0022414 GO:0022414  reproductive process    17     17/58
##                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0000003                                                                                                                                                                                                                          BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/PTCH1
## GO:0002376                                                                                                                                          BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/LCN2/ANXA1/SYK
## GO:0008152                                         BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
## GO:0016032                                                                                                                                                                                                                                                                                                    BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414                                                                                                                                                                                                                                BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/PTCH1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    38     38/58
## GO:0044423 GO:0044423           virion component     0      0/58
## GO:0110165 GO:0110165 cellular anatomical entity    57     57/58
##                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0032991                                                                                                               BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/SYK
## GO:0044423                                                                                                                                                                                                                                                                                                                                    
## GO:0110165 BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/LCN2/PTCH1/ANXA1/SYK
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/71
## GO:0003824 GO:0003824           catalytic activity    34     34/71
## GO:0005198 GO:0005198 structural molecule activity     3      3/71
## GO:0005215 GO:0005215         transporter activity     3      3/71
## GO:0005488 GO:0005488                      binding    70     70/71
## GO:0009055 GO:0009055   electron transfer activity     0      0/71
##                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                          MYH9
## GO:0003824                                                                                                                                                                                                               CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/NCOA3/EZH2/RAF1/TYMS/MAPK8/ERCC1/SETD2/PRKCD/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/PRKAA1/RET/INPP4B/CASP8/SYK
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                             CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                               BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    20     20/71
## GO:0002376 GO:0002376 immune system process    39     39/71
## GO:0008152 GO:0008152     metabolic process    63     63/71
## GO:0009987 GO:0009987      cellular process    70     70/71
## GO:0016032 GO:0016032         viral process     7      7/71
## GO:0022414 GO:0022414  reproductive process    19     19/71
##                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0000003                                                                                                                                                                                                                                                                                        STAT3/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/ERCC1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376                                                                                                                                                                                 CDKN1A/MYC/STAT3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/EZH2/RAF1/FOXO3/MAPK8/NDRG1/PECAM1/ERCC1/SETD2/PRKCD/AKT1/MAPK9/PREX1/RET/CASP8/YWHAE/LCN2/ANXA1/SYK
## GO:0008152                                              CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/CHEK1/ACACA/WWTR1/CDK1/EEF2K/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                              BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414                                                                                                                                                                                                                                                                                              BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/ERCC1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    45     45/71
## GO:0044423 GO:0044423           virion component     0      0/71
## GO:0110165 GO:0110165 cellular anatomical entity    70     70/71
##                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0032991                                                                                                                                                 CDKN1A/MYC/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/ERCC1/AKT1/RAD51/TSC2/CHEK1/WWTR1/CDK1/BCL2L1/PRKAA1/FOXM1/RET/CASP8/SYK
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                              
## GO:0110165 CDKN1A/MYC/VHL/STAT3/DVL3/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/MAPK8/RPS6/SRSF1/NDRG1/ANLN/PECAM1/ERCC1/YWHAB/SETD2/PRKCD/AKT1/RAD51/MAPK9/TSC2/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/PRKAA1/FOXM1/PREX1/RET/INPP4B/CASP8/YWHAE/LCN2/PTCH1/ANXA1/SYK
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/8
## GO:0003824 GO:0003824           catalytic activity     4       4/8
## GO:0005198 GO:0005198 structural molecule activity     0       0/8
## GO:0005215 GO:0005215         transporter activity     0       0/8
## GO:0005488 GO:0005488                      binding     8       8/8
## GO:0009055 GO:0009055   electron transfer activity     0       0/8
##                                                 geneID
## GO:0003774                                            
## GO:0003824                        MAPK3/CHEK1/XIAP/RET
## GO:0005198                                            
## GO:0005215                                            
## GO:0005488 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009055                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/8
## GO:0002376 GO:0002376 immune system process     6       6/8
## GO:0008152 GO:0008152     metabolic process     8       8/8
## GO:0009987 GO:0009987      cellular process     8       8/8
## GO:0016032 GO:0016032         viral process     1       1/8
## GO:0022414 GO:0022414  reproductive process     0       0/8
##                                                 geneID
## GO:0000003                                            
## GO:0002376             MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0016032                                        TFRC
## GO:0022414                                            
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     4       4/8
## GO:0044423 GO:0044423           virion component     0       0/8
## GO:0110165 GO:0110165 cellular anatomical entity     8       8/8
##                                                 geneID
## GO:0032991                        CHEK1/FOXM1/RET/TFRC
## GO:0044423                                            
## GO:0110165 MAPK3/CHEK1/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/5
## GO:0003824 GO:0003824           catalytic activity     2       2/5
## GO:0005198 GO:0005198 structural molecule activity     0       0/5
## GO:0005215 GO:0005215         transporter activity     0       0/5
## GO:0005488 GO:0005488                      binding     5       5/5
## GO:0009055 GO:0009055   electron transfer activity     0       0/5
##                                 geneID
## GO:0003774                            
## GO:0003824                  MAPK3/XIAP
## GO:0005198                            
## GO:0005215                            
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0009055                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/5
## GO:0002376 GO:0002376 immune system process     4       4/5
## GO:0008152 GO:0008152     metabolic process     5       5/5
## GO:0009987 GO:0009987      cellular process     5       5/5
## GO:0016032 GO:0016032         viral process     1       1/5
## GO:0022414 GO:0022414  reproductive process     0       0/5
##                                 geneID
## GO:0000003                            
## GO:0002376       MAPK3/XIAP/TFRC/ANXA1
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC/ANXA1
## GO:0016032                        TFRC
## GO:0022414                            
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/5
## GO:0044423 GO:0044423           virion component     0       0/5
## GO:0110165 GO:0110165 cellular anatomical entity     5       5/5
##                                 geneID
## GO:0032991                  FOXM1/TFRC
## GO:0044423                            
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/20
## GO:0003824 GO:0003824           catalytic activity    11     11/20
## GO:0005198 GO:0005198 structural molecule activity     1      1/20
## GO:0005215 GO:0005215         transporter activity     0      0/20
## GO:0005488 GO:0005488                      binding    19     19/20
## GO:0009055 GO:0009055   electron transfer activity     0      0/20
##                                                                                                                 geneID
## GO:0003774                                                                                                            
## GO:0003824                                                 AKT1/RAD51/MAPK9/MAPK3/CHEK1/ACACA/CDK1/EEF2K/TYMS/XIAP/RET
## GO:0005198                                                                                                       CLDN7
## GO:0005215                                                                                                            
## GO:0005488 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055                                                                                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/20
## GO:0002376 GO:0002376 immune system process     8      8/20
## GO:0008152 GO:0008152     metabolic process    16     16/20
## GO:0009987 GO:0009987      cellular process    19     19/20
## GO:0016032 GO:0016032         viral process     3      3/20
## GO:0022414 GO:0022414  reproductive process     4      4/20
##                                                                                                                 geneID
## GO:0000003                                                                                      AKT1/RAD51/CDK1/BCL2L1
## GO:0002376                                                                  AKT1/MAPK9/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152                    AKT1/RAD51/MAPK9/MAPK3/CHEK1/ACACA/WWTR1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032                                                                                              AKT1/CDK1/TFRC
## GO:0022414                                                                                      AKT1/RAD51/CDK1/BCL2L1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     9      9/20
## GO:0044423 GO:0044423           virion component     0      0/20
## GO:0110165 GO:0110165 cellular anatomical entity    19     19/20
##                                                                                                                 geneID
## GO:0032991                                                           AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/TFRC
## GO:0044423                                                                                                            
## GO:0110165 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     2      2/98
## GO:0003824 GO:0003824           catalytic activity    45     45/98
## GO:0005198 GO:0005198 structural molecule activity     5      5/98
## GO:0005215 GO:0005215         transporter activity     3      3/98
## GO:0005488 GO:0005488                      binding    97     97/98
## GO:0009055 GO:0009055   electron transfer activity     0      0/98
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    MYH9/MYH11
## GO:0003824                                                                                                                                                                                                                                                                                                                CDKN1A/VHL/XIAP/CDK1/AKT1/ACACA/ERBB2/AXL/CASP3/PARP1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/PTEN/NCOA3/EZH2/RAF1/TYMS/EEF2/GSK3B/MSH6/MAPK1/MAPK8/TUBA1B/ERCC1/SETD2/GSK3A/PRKCD/RAD51/MAPK9/CHEK1/EEF2K/PRKAA1/RET/FASN/INPP4B/CASP8/RPS6KA1/LCK/CASP9/SYK
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CLDN7/CTNNA1/RPS6/TUBA1B/MYH11
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    25     25/98
## GO:0002376 GO:0002376 immune system process    50     50/98
## GO:0008152 GO:0008152     metabolic process    87     87/98
## GO:0009987 GO:0009987      cellular process    97     97/98
## GO:0016032 GO:0016032         viral process    11     11/98
## GO:0022414 GO:0022414  reproductive process    24     24/98
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0000003                                                                                                                                                                                                                                                                                                                                                                                                                           NOTCH1/CDK1/STAT3/AKT1/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/PTEN/MYH9/FOXO3/BCL2L1/CTNNA1/GATA3/MSH6/ERCC1/GSK3A/RAD51/CASP8/PTCH1
## GO:0002376                                                                                                                                                                                                                                                                                CDKN1A/MYC/NOTCH1/XIAP/BECN1/STAT3/AKT1/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/EZH2/RAF1/FOXO3/GATA3/MSH6/MAPK1/MAPK8/NDRG1/PECAM1/ERCC1/TP53BP1/SETD2/PRKCD/MAPK9/PREX1/RET/RBM15/XBP1/CASP8/YWHAE/TSC1/LCN2/LCK/ANXA1/ARID1A/SYK
## GO:0008152                                                                 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/ANXA7/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0009987 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     NOTCH1/CDK1/BECN1/AKT1/BCL2/AXL/TP53/TFRC/JUN/GSK3B/GSK3A
## GO:0022414                                                                                                                                                                                                                                                                                                                                                                                                                                 NOTCH1/CDK1/AKT1/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/PTEN/MYH9/FOXO3/BCL2L1/CTNNA1/GATA3/MSH6/ERCC1/GSK3A/RAD51/CASP8/PTCH1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    64     64/98
## GO:0044423 GO:0044423           virion component     0      0/98
## GO:0110165 GO:0110165 cellular anatomical entity    97     97/98
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0032991                                                                                                                                                                                              CDKN1A/MYC/NOTCH1/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/NCOA3/MYH9/IRS1/JUN/EZH2/FOXO3/BCL2L1/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/RPS6/SRSF1/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/GSK3A/RAD51/TSC2/CHEK1/WWTR1/E2F1/CCNB1/PRKAA1/FOXM1/RET/RBM15/XBP1/MYH11/CASP8/TSC1/ARID1A/CASP9/SYK
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## GO:0110165 CDKN1A/MYC/VHL/NOTCH1/XIAP/CDK1/YBX1/BECN1/STAT3/DVL3/PEA15/AKT1/ACACA/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/PARP1/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/PTEN/NCOA3/MYH9/IRS1/JUN/EZH2/RAF1/TYMS/FOXO3/BCL2L1/ANXA7/CLDN7/CTNNA1/EEF2/EIF4G1/GATA3/GSK3B/MSH6/NRG1/MAPK1/MAPK8/RPS6/SRSF1/TUBA1B/NDRG1/ANLN/AKT1S1/RICTOR/PECAM1/ERCC1/TP53BP1/YWHAB/SETD2/GSK3A/PRKCD/RAD51/MAPK9/TSC2/STMN1/CHEK1/WWTR1/EEF2K/E2F1/CCNB1/PRKAA1/FOXM1/PREX1/RET/RBM15/FASN/INPP4B/XBP1/MYH11/CASP8/RPS6KA1/YWHAE/TSC1/LCN2/TTF1/LCK/PTCH1/ANXA1/ARID1A/CASP9/SYK
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/8
## GO:0003824 GO:0003824           catalytic activity     3       3/8
## GO:0005198 GO:0005198 structural molecule activity     1       1/8
## GO:0005215 GO:0005215         transporter activity     0       0/8
## GO:0005488 GO:0005488                      binding     8       8/8
## GO:0009055 GO:0009055   electron transfer activity     0       0/8
##                                                 geneID
## GO:0003774                                            
## GO:0003824                              MAPK3/XIAP/RET
## GO:0005198                                       CLDN7
## GO:0005215                                            
## GO:0005488 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/8
## GO:0002376 GO:0002376 immune system process     6       6/8
## GO:0008152 GO:0008152     metabolic process     7       7/8
## GO:0009987 GO:0009987      cellular process     8       8/8
## GO:0016032 GO:0016032         viral process     1       1/8
## GO:0022414 GO:0022414  reproductive process     0       0/8
##                                                 geneID
## GO:0000003                                            
## GO:0002376             MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152       MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032                                        TFRC
## GO:0022414                                            
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/8
## GO:0044423 GO:0044423           virion component     0       0/8
## GO:0110165 GO:0110165 cellular anatomical entity     8       8/8
##                                                 geneID
## GO:0032991                              FOXM1/RET/TFRC
## GO:0044423                                            
## GO:0110165 MAPK3/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/23
## GO:0003824 GO:0003824           catalytic activity    13     13/23
## GO:0005198 GO:0005198 structural molecule activity     2      2/23
## GO:0005215 GO:0005215         transporter activity     2      2/23
## GO:0005488 GO:0005488                      binding    23     23/23
## GO:0009055 GO:0009055   electron transfer activity     0      0/23
##                                                                                                                                geneID
## GO:0003774                                                                                                                           
## GO:0003824                                                        MET/G6PD/KRAS/CCND1/AKT1/IGF1R/CHEK1/PRKCD/TGM2/EEF2K/TYMS/XIAP/RET
## GO:0005198                                                                                                                  FN1/CLDN7
## GO:0005215                                                                                                                 BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
## GO:0009055                                                                                                                           
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/23
## GO:0002376 GO:0002376 immune system process    14     14/23
## GO:0008152 GO:0008152     metabolic process    22     22/23
## GO:0009987 GO:0009987      cellular process    23     23/23
## GO:0016032 GO:0016032         viral process     3      3/23
## GO:0022414 GO:0022414  reproductive process     5      5/23
##                                                                                                                                geneID
## GO:0000003                                                                                                 ESR1/BCL2/AKT1/IGF1R/FOXO3
## GO:0002376                                                   ESR1/G6PD/BCL2/AKT1/IGF1R/FOXO3/FN1/PRKCD/XIAP/PREX1/RET/TFRC/LCN2/ANXA1
## GO:0008152       ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/LCN2/ANXA1
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
## GO:0016032                                                                                                             BCL2/AKT1/TFRC
## GO:0022414                                                                                                 ESR1/BCL2/AKT1/IGF1R/FOXO3
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/23
## GO:0044423 GO:0044423           virion component     0      0/23
## GO:0110165 GO:0110165 cellular anatomical entity    23     23/23
##                                                                                                                                geneID
## GO:0032991                                                        ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/TGM2/RET/TFRC
## GO:0044423                                                                                                                           
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/FOXO3/CHEK1/FN1/PRKCD/TGM2/EEF2K/TYMS/XIAP/PREX1/RET/TFRC/CLDN7/LCN2/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/60
## GO:0003824 GO:0003824           catalytic activity    27     27/60
## GO:0005198 GO:0005198 structural molecule activity     3      3/60
## GO:0005215 GO:0005215         transporter activity     3      3/60
## GO:0005488 GO:0005488                      binding    59     59/60
## GO:0009055 GO:0009055   electron transfer activity     0      0/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                          MYH9
## GO:0003824                                                                                                                                                                                          CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/CASP8/SYK
## GO:0005198                                                                                                                                                                                                                                                                                                                             CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                               BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009055                                                                                                                                                                                                                                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/60
## GO:0002376 GO:0002376 immune system process    34     34/60
## GO:0008152 GO:0008152     metabolic process    53     53/60
## GO:0009987 GO:0009987      cellular process    59     59/60
## GO:0016032 GO:0016032         viral process     7      7/60
## GO:0022414 GO:0022414  reproductive process    18     18/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0000003                                                                                                                                                                                                                              BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376                                                                                                                                              CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/CASP8/LCN2/ANXA1/SYK
## GO:0008152                                         CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0016032                                                                                                                                                                                                                                                                                                              BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414                                                                                                                                                                                                                                    BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    39     39/60
## GO:0044423 GO:0044423           virion component     0      0/60
## GO:0110165 GO:0110165 cellular anatomical entity    59     59/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0032991                                                                                                                   CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/CASP8/SYK
## GO:0044423                                                                                                                                                                                                                                                                                                                                              
## GO:0110165 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/60
## GO:0003824 GO:0003824           catalytic activity    27     27/60
## GO:0005198 GO:0005198 structural molecule activity     3      3/60
## GO:0005215 GO:0005215         transporter activity     3      3/60
## GO:0005488 GO:0005488                      binding    59     59/60
## GO:0009055 GO:0009055   electron transfer activity     0      0/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                          MYH9
## GO:0003824                                                                                                                                                                                          CDKN1A/VHL/ERBB2/AXL/CASP3/PARP1/XIAP/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/RAF1/TYMS/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/CDK1/EEF2K/RET/CASP8/SYK
## GO:0005198                                                                                                                                                                                                                                                                                                                             CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                               BCL2/BAK1/IGF1R
## GO:0005488 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009055                                                                                                                                                                                                                                                                                                                                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/60
## GO:0002376 GO:0002376 immune system process    34     34/60
## GO:0008152 GO:0008152     metabolic process    53     53/60
## GO:0009987 GO:0009987      cellular process    59     59/60
## GO:0016032 GO:0016032         viral process     7      7/60
## GO:0022414 GO:0022414  reproductive process    18     18/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0000003                                                                                                                                                                                                                              BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
## GO:0002376                                                                                                                                              CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/RAF1/FOXO3/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PREX1/RET/CASP8/LCN2/ANXA1/SYK
## GO:0008152                                         CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/CHEK1/ACACA/WWTR1/CDK1/EEF2K/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0009987 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
## GO:0016032                                                                                                                                                                                                                                                                                                              BCL2/AXL/TP53/TFRC/JUN/AKT1/CDK1
## GO:0022414                                                                                                                                                                                                                                    BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/IGF1R/PIK3CA/MYH9/FOXO3/CTNNA1/AKT1/RAD51/CDK1/BCL2L1/CASP8/PTCH1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    39     39/60
## GO:0044423 GO:0044423           virion component     0      0/60
## GO:0110165 GO:0110165 cellular anatomical entity    59     59/60
##                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0032991                                                                                                                   CDKN1A/MYC/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/IGF1R/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/IRS1/JUN/FOXO3/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/RAD51/CHEK1/WWTR1/CDK1/BCL2L1/FOXM1/RET/CASP8/SYK
## GO:0044423                                                                                                                                                                                                                                                                                                                                              
## GO:0110165 CDKN1A/MYC/VHL/BCL2/ERBB2/AXL/BAK1/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/IGF1R/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/IRS1/JUN/RAF1/TYMS/FOXO3/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/RAD51/MAPK9/STMN1/CHEK1/ACACA/WWTR1/CDK1/EEF2K/BCL2L1/FOXM1/PREX1/RET/CASP8/LCN2/PTCH1/ANXA1/SYK
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/6
## GO:0003824 GO:0003824           catalytic activity     2       2/6
## GO:0005198 GO:0005198 structural molecule activity     0       0/6
## GO:0005215 GO:0005215         transporter activity     0       0/6
## GO:0005488 GO:0005488                      binding     6       6/6
## GO:0009055 GO:0009055   electron transfer activity     0       0/6
##                                       geneID
## GO:0003774                                  
## GO:0003824                        MAPK3/XIAP
## GO:0005198                                  
## GO:0005215                                  
## GO:0005488 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/6
## GO:0002376 GO:0002376 immune system process     5       5/6
## GO:0008152 GO:0008152     metabolic process     6       6/6
## GO:0009987 GO:0009987      cellular process     6       6/6
## GO:0016032 GO:0016032         viral process     1       1/6
## GO:0022414 GO:0022414  reproductive process     0       0/6
##                                       geneID
## GO:0000003                                  
## GO:0002376       MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032                              TFRC
## GO:0022414                                  
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/6
## GO:0044423 GO:0044423           virion component     0       0/6
## GO:0110165 GO:0110165 cellular anatomical entity     6       6/6
##                                       geneID
## GO:0032991                        FOXM1/TFRC
## GO:0044423                                  
## GO:0110165 MAPK3/FOXM1/XIAP/PREX1/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/15
## GO:0003824 GO:0003824           catalytic activity     8      8/15
## GO:0005198 GO:0005198 structural molecule activity     1      1/15
## GO:0005215 GO:0005215         transporter activity     0      0/15
## GO:0005488 GO:0005488                      binding    15     15/15
## GO:0009055 GO:0009055   electron transfer activity     0      0/15
##                                                                                       geneID
## GO:0003774                                                                                  
## GO:0003824                                        CDKN1A/VHL/AKT1/MAPK3/RAB11B/TYMS/XIAP/RET
## GO:0005198                                                                             CLDN7
## GO:0005215                                                                                  
## GO:0005488 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055                                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1      1/15
## GO:0002376 GO:0002376 immune system process     9      9/15
## GO:0008152 GO:0008152     metabolic process    14     14/15
## GO:0009987 GO:0009987      cellular process    15     15/15
## GO:0016032 GO:0016032         viral process     2      2/15
## GO:0022414 GO:0022414  reproductive process     1      1/15
##                                                                                       geneID
## GO:0000003                                                                              AKT1
## GO:0002376                                   CDKN1A/MYC/AKT1/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152       CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032                                                                         AKT1/TFRC
## GO:0022414                                                                              AKT1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     7      7/15
## GO:0044423 GO:0044423           virion component     0      0/15
## GO:0110165 GO:0110165 cellular anatomical entity    15     15/15
##                                                                                       geneID
## GO:0032991                                              CDKN1A/MYC/AKT1/WWTR1/FOXM1/RET/TFRC
## GO:0044423                                                                                  
## GO:0110165 CDKN1A/MYC/VHL/AKT1/MAPK3/WWTR1/RAB11B/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[12]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                               Description GeneRatio
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     10/57
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      5/57
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     10/57
## GO:0051400 GO:0051400                         BH domain binding      3/57
## GO:0045296 GO:0045296                          cadherin binding      8/57
## GO:0051219 GO:0051219                    phosphoprotein binding      5/57
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 6.260798e-07 0.0001582086 8.353543e-05
## GO:0045309  59/18522 1.017419e-06 0.0001582086 8.353543e-05
## GO:0140297 478/18522 1.736820e-06 0.0001781183 9.404791e-05
## GO:0051400   9/18522 2.290911e-06 0.0001781183 9.404791e-05
## GO:0045296 333/18522 7.702656e-06 0.0004791052 2.529714e-04
## GO:0051219  93/18522 9.754331e-06 0.0005055995 2.669606e-04
##                                                             geneID Count
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK    10
## GO:0045309                              YWHAZ/MAPK3/IRS1/YWHAB/SYK     5
## GO:0140297   BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN    10
## GO:0051400                                        BCL2/BAK1/BCL2L1     3
## GO:0045296        YWHAZ/CTNNB1/PRDX1/MYH9/CTNNA1/NDRG1/YWHAB/ANXA1     8
## GO:0051219                              YWHAZ/MAPK3/IRS1/YWHAB/SYK     5
##                    ID                                 Description GeneRatio
## GO:0097305 GO:0097305                         response to alcohol     16/57
## GO:0010332 GO:0010332                 response to gamma radiation      8/57
## GO:2001233 GO:2001233   regulation of apoptotic signaling pathway     14/57
## GO:0010212 GO:0010212              response to ionizing radiation     10/57
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     13/57
## GO:0104004 GO:0104004 cellular response to environmental stimulus     13/57
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0097305 259/18888 3.441790e-17 1.106880e-13 4.836620e-14
## GO:0010332  52/18888 2.800084e-12 4.502535e-09 1.967427e-09
## GO:2001233 396/18888 8.562686e-12 7.890099e-09 3.447657e-09
## GO:0010212 138/18888 1.004845e-11 7.890099e-09 3.447657e-09
## GO:0071214 334/18888 1.593278e-11 7.890099e-09 3.447657e-09
## GO:0104004 334/18888 1.593278e-11 7.890099e-09 3.447657e-09
##                                                                                                      geneID
## GO:0097305 BAK1/PARP1/CTNNB1/IGF1R/CDKN1A/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/PTCH1
## GO:0010332                                                      BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/BCL2L1
## GO:2001233                   BCL2/BAK1/MYC/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212                                          BCL2/BAK1/MYC/CASP3/TP53/YAP1/PARP1/CDKN1A/RAD51/BCL2L1
## GO:0071214                      BAK1/MYC/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/CDKN1A/RAD51/CHEK1/BCL2L1
## GO:0104004                      BAK1/MYC/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/CDKN1A/RAD51/CHEK1/BCL2L1
##            Count
## GO:0097305    16
## GO:0010332     8
## GO:2001233    14
## GO:0010212    10
## GO:0071214    13
## GO:0104004    13
##                    ID                                       Description
## GO:0097136 GO:0097136                      Bcl-2 family protein complex
## GO:0005901 GO:0005901                                           caveola
## GO:0044853 GO:0044853                              plasma membrane raft
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0045121 GO:0045121                                     membrane raft
## GO:0098857 GO:0098857                              membrane microdomain
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097136      4/57  10/19894 1.255224e-08 3.037641e-06 1.730887e-06
## GO:0005901      6/57  82/19894 1.249512e-07 1.511910e-05 8.615057e-06
## GO:0044853      6/57 113/19894 8.421415e-07 6.793275e-05 3.870896e-05
## GO:0090571      3/57  15/19894 9.901927e-06 5.990666e-04 3.413559e-04
## GO:0045121      7/57 286/19894 1.686241e-05 6.955836e-04 3.963526e-04
## GO:0098857      7/57 287/19894 1.724587e-05 6.955836e-04 3.963526e-04
##                                                 geneID Count
## GO:0097136                    BCL2/BAK1/BCL2L11/BCL2L1     4
## GO:0005901        CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0044853        CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0090571                            MYC/CTNNB1/FOXO3     3
## GO:0045121 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PECAM1/PTCH1     7
## GO:0098857 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PECAM1/PTCH1     7
##                    ID                               Description GeneRatio
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     13/70
## GO:0019902 GO:0019902                       phosphatase binding      9/70
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      6/70
## GO:0106310 GO:0106310            protein serine kinase activity     11/70
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     12/70
## GO:0045296 GO:0045296                          cadherin binding     10/70
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 6.238592e-09 2.258370e-06 1.090112e-06
## GO:0019902 189/18522 3.770640e-08 6.824858e-06 3.294349e-06
## GO:0045309  59/18522 9.009728e-08 9.808537e-06 4.734566e-06
## GO:0106310 363/18522 1.083816e-07 9.808537e-06 4.734566e-06
## GO:0140297 478/18522 2.081173e-07 1.506770e-05 7.273153e-06
## GO:0045296 333/18522 4.702482e-07 2.837164e-05 1.369495e-05
##                                                                                geneID
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/MAPK8/PRKCD/AKT1/MAPK9/CHEK1/CDK1/EEF2K/PRKAA1/SYK
## GO:0019902                          STAT3/BCL2/TP53/CTNNB1/MAPK3/MAPK8/TSC2/YWHAE/SYK
## GO:0045309                                           YWHAZ/MAPK3/IRS1/YWHAB/YWHAE/SYK
## GO:0106310           PIK3CA/PRKCA/MAPK3/RAF1/MAPK8/PRKCD/AKT1/MAPK9/CHEK1/CDK1/PRKAA1
## GO:0140297            MYC/VHL/STAT3/BCL2/TP53/YAP1/YWHAZ/PARP1/CTNNB1/MAPK3/NCOA3/JUN
## GO:0045296                YWHAZ/CTNNB1/PRDX1/MYH9/CTNNA1/NDRG1/ANLN/YWHAB/YWHAE/ANXA1
##            Count
## GO:0004674    13
## GO:0019902     9
## GO:0045309     6
## GO:0106310    11
## GO:0140297    12
## GO:0045296    10
##                    ID                                 Description GeneRatio
## GO:0097305 GO:0097305                         response to alcohol     18/70
## GO:0000302 GO:0000302         response to reactive oxygen species     15/70
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     17/70
## GO:0104004 GO:0104004 cellular response to environmental stimulus     17/70
## GO:0006979 GO:0006979                response to oxidative stress     18/70
## GO:0062197 GO:0062197        cellular response to chemical stress     16/70
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0097305 259/18888 1.992636e-18 6.954300e-15 3.085440e-15
## GO:0000302 203/18888 7.514826e-16 1.311337e-12 5.818058e-13
## GO:0071214 334/18888 3.632063e-15 2.722327e-12 1.207825e-12
## GO:0104004 334/18888 3.632063e-15 2.722327e-12 1.207825e-12
## GO:0006979 398/18888 3.900182e-15 2.722327e-12 1.207825e-12
## GO:0062197 311/18888 2.210193e-14 1.285596e-11 5.703850e-12
##                                                                                                                   geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/PRKAA1/CASP8/PTCH1
## GO:0000302                             BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK8/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
## GO:0071214           CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/MAPK8/ERCC1/PRKCD/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004           CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/MAPK8/ERCC1/PRKCD/RAD51/CHEK1/BCL2L1/CASP8
## GO:0006979            BCL2/AXL/BAK1/CASP3/TP53/PARP1/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK8/ERCC1/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
## GO:0062197                     AXL/CASP3/TP53/PARP1/PRDX1/PIK3CA/MAPK3/JUN/EZH2/FOXO3/MAPK8/PRKCD/AKT1/MAPK9/CDK1/PRKAA1
##            Count
## GO:0097305    18
## GO:0000302    15
## GO:0071214    17
## GO:0104004    17
## GO:0006979    18
## GO:0062197    16
##                    ID                                       Description
## GO:0097136 GO:0097136                      Bcl-2 family protein complex
## GO:0005901 GO:0005901                                           caveola
## GO:0044853 GO:0044853                              plasma membrane raft
## GO:0005741 GO:0005741                      mitochondrial outer membrane
## GO:0005925 GO:0005925                                    focal adhesion
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097136      4/70  10/19894 2.904473e-08 7.754944e-06 4.647157e-06
## GO:0005901      6/70  82/19894 4.326477e-07 5.775846e-05 3.461181e-05
## GO:0044853      6/70 113/19894 2.865901e-06 2.550652e-04 1.528481e-04
## GO:0005741      7/70 219/19894 1.184844e-05 7.451852e-04 4.465529e-04
## GO:0005925      9/70 421/19894 1.622931e-05 7.451852e-04 4.465529e-04
## GO:0090571      3/70  15/19894 1.841593e-05 7.451852e-04 4.465529e-04
##                                                           geneID Count
## GO:0097136                              BCL2/BAK1/BCL2L11/BCL2L1     4
## GO:0005901                  CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0044853                  CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0005741             BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
## GO:0005925 YWHAZ/CTNNB1/MAPK3/TGM2/MYH9/CTNNA1/YWHAB/YWHAE/ANXA1     9
## GO:0090571                                      MYC/CTNNB1/FOXO3     3
##                    ID                             Description GeneRatio
## GO:0004998 GO:0004998           transferrin receptor activity       1/8
## GO:0035402 GO:0035402           histone H3T11 kinase activity       1/8
## GO:0019834 GO:0019834     phospholipase A2 inhibitor activity       1/8
## GO:0120283 GO:0120283 protein serine/threonine kinase binding       1/8
## GO:0004859 GO:0004859        phospholipase inhibitor activity       1/8
## GO:0140996 GO:0140996              histone H3 kinase activity       1/8
##             BgRatio       pvalue   p.adjust      qvalue geneID Count
## GO:0004998  2/18522 0.0008636744 0.02288737 0.009091309   TFRC     1
## GO:0035402  2/18522 0.0008636744 0.02288737 0.009091309  CHEK1     1
## GO:0019834  4/18522 0.0017266959 0.03050496 0.012117165  ANXA1     1
## GO:0120283  7/18522 0.0030200053 0.04001507 0.015894765   XIAP     1
## GO:0004859 11/18522 0.0047421371 0.04188888 0.016639078  ANXA1     1
## GO:0140996 11/18522 0.0047421371 0.04188888 0.016639078  CHEK1     1
##                    ID                                    Description GeneRatio
## GO:0050900 GO:0050900                            leukocyte migration       4/8
## GO:0071621 GO:0071621                         granulocyte chemotaxis       3/8
## GO:0045785 GO:0045785           positive regulation of cell adhesion       4/8
## GO:0097530 GO:0097530                          granulocyte migration       3/8
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation       3/8
## GO:0042770 GO:0042770  signal transduction in response to DNA damage       3/8
##              BgRatio       pvalue    p.adjust      qvalue                geneID
## GO:0050900 396/18888 1.246268e-05 0.005166253 0.002253057 MAPK3/PREX1/RET/ANXA1
## GO:0071621 128/18888 1.660669e-05 0.005166253 0.002253057     MAPK3/PREX1/ANXA1
## GO:0045785 485/18888 2.769198e-05 0.005166253 0.002253057  PREX1/RET/TFRC/ANXA1
## GO:0097530 154/18888 2.888705e-05 0.005166253 0.002253057     MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 3.486001e-05 0.005166253 0.002253057      MAPK3/TFRC/ANXA1
## GO:0042770 188/18888 5.238574e-05 0.006369700 0.002777893     MAPK3/CHEK1/FOXM1
##            Count
## GO:0050900     4
## GO:0071621     3
## GO:0045785     4
## GO:0097530     3
## GO:0070665     3
## GO:0042770     3
##                    ID    Description GeneRatio   BgRatio       pvalue
## GO:0005769 GO:0005769 early endosome       4/8 428/19894 1.380895e-05
##                p.adjust       qvalue               geneID Count
## GO:0005769 0.0007456833 0.0004506078 MAPK3/RET/TFRC/ANXA1     4
##                    ID                             Description GeneRatio
## GO:0004998 GO:0004998           transferrin receptor activity       1/5
## GO:0019834 GO:0019834     phospholipase A2 inhibitor activity       1/5
## GO:0120283 GO:0120283 protein serine/threonine kinase binding       1/5
## GO:0004859 GO:0004859        phospholipase inhibitor activity       1/5
## GO:0055102 GO:0055102               lipase inhibitor activity       1/5
## GO:0004857 GO:0004857               enzyme inhibitor activity       2/5
##              BgRatio       pvalue   p.adjust      qvalue     geneID Count
## GO:0004998   2/18522 0.0005398402 0.02266839 0.006249431       TFRC     1
## GO:0019834   4/18522 0.0010794472 0.02266839 0.006249431      ANXA1     1
## GO:0120283   7/18522 0.0018884208 0.02514362 0.006931825       XIAP     1
## GO:0004859  11/18522 0.0029662367 0.02514362 0.006931825      ANXA1     1
## GO:0055102  15/18522 0.0040431214 0.02514362 0.006931825      ANXA1     1
## GO:0004857 389/18522 0.0042187412 0.02514362 0.006931825 XIAP/ANXA1     2
##                    ID
## GO:0070665 GO:0070665
## GO:0070663 GO:0070663
## GO:0032872 GO:0032872
## GO:0051054 GO:0051054
## GO:0070302 GO:0070302
## GO:0070661 GO:0070661
##                                                                Description
## GO:0070665                  positive regulation of leukocyte proliferation
## GO:0070663                           regulation of leukocyte proliferation
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0070661                                         leukocyte proliferation
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0070665       3/5 164/18888 6.345810e-06 0.003540962 0.001035369
## GO:0070663       3/5 267/18888 2.735257e-05 0.004381714 0.001281203
## GO:0032872       2/5  35/18888 3.324142e-05 0.004381714 0.001281203
## GO:0051054       3/5 301/18888 3.913209e-05 0.004381714 0.001281203
## GO:0070302       2/5  38/18888 3.926267e-05 0.004381714 0.001281203
## GO:0070661       3/5 352/18888 6.241821e-05 0.005446835 0.001592642
##                      geneID Count
## GO:0070665 MAPK3/TFRC/ANXA1     3
## GO:0070663 MAPK3/TFRC/ANXA1     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0051054 MAPK3/FOXM1/TFRC     3
## GO:0070302      MAPK3/FOXM1     2
## GO:0070661 MAPK3/TFRC/ANXA1     3
##                    ID                      Description GeneRatio   BgRatio
## GO:0005769 GO:0005769                   early endosome       3/5 428/19894
## GO:0016323 GO:0016323      basolateral plasma membrane       2/5 255/19894
## GO:0009925 GO:0009925            basal plasma membrane       2/5 286/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/5   8/19894
## GO:0045178 GO:0045178               basal part of cell       2/5 305/19894
## GO:0005925 GO:0005925                   focal adhesion       2/5 421/19894
##                  pvalue    p.adjust      qvalue           geneID Count
## GO:0005769 9.575381e-05 0.004117414 0.001814283 MAPK3/TFRC/ANXA1     3
## GO:0016323 1.595396e-03 0.019541951 0.008610897       TFRC/ANXA1     2
## GO:0009925 2.001441e-03 0.019541951 0.008610897       TFRC/ANXA1     2
## GO:1990712 2.009242e-03 0.019541951 0.008610897             TFRC     1
## GO:0045178 2.272320e-03 0.019541951 0.008610897       TFRC/ANXA1     2
## GO:0005925 4.282683e-03 0.024274850 0.010696384      MAPK3/ANXA1     2
##                    ID                                       Description
## GO:0004674 GO:0004674          protein serine/threonine kinase activity
## GO:0106310 GO:0106310                    protein serine kinase activity
## GO:0004707 GO:0004707                               MAP kinase activity
## GO:0035173 GO:0035173                           histone kinase activity
## GO:0004712 GO:0004712 protein serine/threonine/tyrosine kinase activity
## GO:0030544 GO:0030544                             Hsp70 protein binding
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0004674      6/19 427/18522 3.048491e-06 0.000353625 0.0001829095
## GO:0106310      5/19 363/18522 2.608195e-05 0.001512753 0.0007824586
## GO:0004707      2/19  16/18522 1.186135e-04 0.004586388 0.0023722695
## GO:0035173      2/19  23/18522 2.490081e-04 0.007221236 0.0037351219
## GO:0004712      2/19  43/18522 8.779498e-04 0.020368435 0.0105353976
## GO:0030544      2/19  51/18522 1.233584e-03 0.023787161 0.0123037041
##                                       geneID Count
## GO:0004674 AKT1/MAPK9/MAPK3/CHEK1/CDK1/EEF2K     6
## GO:0106310       AKT1/MAPK9/MAPK3/CHEK1/CDK1     5
## GO:0004707                       MAPK9/MAPK3     2
## GO:0035173                        CHEK1/CDK1     2
## GO:0004712                        AKT1/MAPK9     2
## GO:0030544                         CDK1/TFRC     2
##                    ID                                            Description
## GO:0097305 GO:0097305                                    response to alcohol
## GO:0046686 GO:0046686                                response to cadmium ion
## GO:0051054 GO:0051054           positive regulation of DNA metabolic process
## GO:0042770 GO:0042770          signal transduction in response to DNA damage
## GO:0010038 GO:0010038                                  response to metal ion
## GO:1900182 GO:1900182 positive regulation of protein localization to nucleus
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097305      7/19 259/18888 3.680634e-09 5.675538e-06 2.704298e-06
## GO:0046686      4/19  60/18888 3.440463e-07 1.825118e-04 8.696376e-05
## GO:0051054      6/19 301/18888 3.550813e-07 1.825118e-04 8.696376e-05
## GO:0042770      5/19 188/18888 9.617566e-07 3.119988e-04 1.486621e-04
## GO:0010038      6/19 360/18888 1.011669e-06 3.119988e-04 1.486621e-04
## GO:1900182      4/19  94/18888 2.105488e-06 5.411104e-04 2.578299e-04
##                                             geneID Count
## GO:0097305 AKT1/RAD51/ACACA/CDK1/BCL2L1/TYMS/CLDN7     7
## GO:0046686                   AKT1/MAPK9/MAPK3/CDK1     4
## GO:0051054        AKT1/RAD51/MAPK3/CDK1/FOXM1/TFRC     6
## GO:0042770            RAD51/MAPK3/CHEK1/CDK1/FOXM1     5
## GO:0010038        AKT1/MAPK9/MAPK3/CDK1/EEF2K/TFRC     6
## GO:1900182                    AKT1/WWTR1/CDK1/TFRC     4
##                    ID                  Description GeneRatio   BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region      3/19 173/19894
## GO:0005769 GO:0005769               early endosome      4/19 428/19894
## GO:0005759 GO:0005759         mitochondrial matrix      4/19 491/19894
## GO:0016323 GO:0016323  basolateral plasma membrane      3/19 255/19894
## GO:0016328 GO:0016328      lateral plasma membrane      2/19  68/19894
## GO:0097122 GO:0097122       cyclin A2-CDK1 complex      1/19   2/19894
##                  pvalue p.adjust     qvalue                 geneID Count
## GO:0000781 0.0005652514 0.025775 0.02034869       RAD51/CHEK1/CDK1     3
## GO:0005769 0.0006335653 0.025775 0.02034869   MAPK3/RET/TFRC/ANXA1     4
## GO:0005759 0.0010580319 0.025775 0.02034869 RAD51/CDK1/BCL2L1/TYMS     4
## GO:0016323 0.0017325255 0.025775 0.02034869       TFRC/CLDN7/ANXA1     3
## GO:0016328 0.0018960073 0.025775 0.02034869            CLDN7/ANXA1     2
## GO:0097122 0.0019092595 0.025775 0.02034869                   CDK1     1
##                    ID                               Description GeneRatio
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     17/97
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     17/97
## GO:0106310 GO:0106310            protein serine kinase activity     15/97
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      8/97
## GO:0019902 GO:0019902                       phosphatase binding     11/97
## GO:0044389 GO:0044389     ubiquitin-like protein ligase binding     13/97
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 7.461099e-11 3.357494e-08 1.743541e-08
## GO:0140297 478/18522 4.254302e-10 8.448519e-08 4.387301e-08
## GO:0106310 363/18522 6.535172e-10 8.448519e-08 4.387301e-08
## GO:0045309  59/18522 7.509794e-10 8.448519e-08 4.387301e-08
## GO:0019902 189/18522 4.327426e-09 3.894684e-07 2.022502e-07
## GO:0044389 324/18522 1.408341e-08 1.056256e-06 5.485118e-07
##                                                                                                          geneID
## GO:0004674 CDK1/AKT1/PIK3CA/PRKCA/MAPK3/RAF1/GSK3B/MAPK1/MAPK8/GSK3A/PRKCD/MAPK9/CHEK1/EEF2K/PRKAA1/RPS6KA1/SYK
## GO:0140297      MYC/VHL/STAT3/BCL2/TP53/YAP1/YWHAZ/PARP1/CTNNB1/MAPK3/NCOA3/JUN/GATA3/GSK3B/TP53BP1/E2F1/ARID1A
## GO:0106310           CDK1/AKT1/PIK3CA/PRKCA/MAPK3/RAF1/GSK3B/MAPK1/MAPK8/GSK3A/PRKCD/MAPK9/CHEK1/PRKAA1/RPS6KA1
## GO:0045309                                                           YWHAZ/MAPK3/IRS1/MAPK1/YWHAB/YWHAE/LCK/SYK
## GO:0019902                                          STAT3/BCL2/TP53/CTNNB1/MAPK3/MAPK1/MAPK8/TSC2/YWHAE/LCK/SYK
## GO:0044389                         CDKN1A/BECN1/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/GSK3B/TUBA1B/CCNB1/CASP8/YWHAE
##            Count
## GO:0004674    17
## GO:0140297    17
## GO:0106310    15
## GO:0045309     8
## GO:0019902    11
## GO:0044389    13
##                    ID                                 Description GeneRatio
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     21/97
## GO:0104004 GO:0104004 cellular response to environmental stimulus     21/97
## GO:0031929 GO:0031929                               TOR signaling     16/97
## GO:0018105 GO:0018105             peptidyl-serine phosphorylation     19/97
## GO:0000302 GO:0000302         response to reactive oxygen species     17/97
## GO:0071496 GO:0071496      cellular response to external stimulus     20/97
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071214 334/18888 2.494398e-17 5.106032e-14 2.305348e-14
## GO:0104004 334/18888 2.494398e-17 5.106032e-14 2.305348e-14
## GO:0031929 165/18888 2.365810e-16 2.520865e-13 1.138158e-13
## GO:0018105 282/18888 2.716733e-16 2.520865e-13 1.138158e-13
## GO:0000302 203/18888 3.078731e-16 2.520865e-13 1.138158e-13
## GO:0071496 335/18888 4.257721e-16 2.905185e-13 1.311677e-13
##                                                                                                                                  geneID
## GO:0071214 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/PTEN/BCL2L1/GATA3/MAPK8/ERCC1/TP53BP1/PRKCD/RAD51/CHEK1/CASP8/CASP9
## GO:0104004 CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/PTEN/BCL2L1/GATA3/MAPK8/ERCC1/TP53BP1/PRKCD/RAD51/CHEK1/CASP8/CASP9
## GO:0031929                                VHL/AKT1/YWHAZ/PIK3CA/MAPK3/GATA3/GSK3B/RPS6/AKT1S1/RICTOR/GSK3A/TSC2/PRKAA1/RPS6KA1/TSC1/SYK
## GO:0018105                CDK1/AKT1/BCL2/BAK1/PRKCA/TFRC/PTEN/RAF1/EIF4G1/GSK3B/MAPK1/MAPK8/RICTOR/GSK3A/PRKCD/MAPK9/PRKAA1/RET/RPS6KA1
## GO:0000302                                CDK1/BECN1/AKT1/BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/EZH2/FOXO3/MAPK1/MAPK8/PRKCD/MAPK9/PRKAA1
## GO:0071496          CDKN1A/BECN1/BCL2/AXL/BAK1/TP53/YWHAZ/IGF1R/MAPK3/FOXO3/EIF4G1/MAPK1/MAPK8/RICTOR/TSC2/CHEK1/PRKAA1/XBP1/CASP8/TSC1
##            Count
## GO:0071214    21
## GO:0104004    21
## GO:0031929    16
## GO:0018105    19
## GO:0000302    17
## GO:0071496    20
##                    ID                  Description GeneRatio   BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex      4/97  10/19894
## GO:0005901 GO:0005901                      caveola      7/97  82/19894
## GO:0042470 GO:0042470                   melanosome      7/97 112/19894
## GO:0048770 GO:0048770              pigment granule      7/97 112/19894
## GO:0044853 GO:0044853         plasma membrane raft      7/97 113/19894
## GO:0045121 GO:0045121                membrane raft      9/97 286/19894
##                  pvalue     p.adjust       qvalue
## GO:0097136 1.090420e-07 2.337397e-05 1.468440e-05
## GO:0005901 1.484062e-07 2.337397e-05 1.468440e-05
## GO:0042470 1.255778e-06 8.400528e-05 5.277525e-05
## GO:0048770 1.255778e-06 8.400528e-05 5.277525e-05
## GO:0044853 1.333417e-06 8.400528e-05 5.277525e-05
## GO:0045121 1.094424e-05 4.659951e-04 2.927555e-04
##                                                           geneID Count
## GO:0097136                              BCL2/BAK1/BCL2L11/BCL2L1     4
## GO:0005901            CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PTCH1     7
## GO:0042470               YWHAZ/PRDX1/TFRC/YWHAB/FASN/MYH11/YWHAE     7
## GO:0048770               YWHAZ/PRDX1/TFRC/YWHAB/FASN/MYH11/YWHAE     7
## GO:0044853            CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PTCH1     7
## GO:0045121 CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/MAPK1/PECAM1/LCK/PTCH1     9
##                    ID                             Description GeneRatio BgRatio
## GO:0004998 GO:0004998           transferrin receptor activity       1/8 2/18522
## GO:0019834 GO:0019834     phospholipase A2 inhibitor activity       1/8 4/18522
## GO:0120283 GO:0120283 protein serine/threonine kinase binding       1/8 7/18522
##                  pvalue   p.adjust     qvalue geneID Count
## GO:0004998 0.0008636744 0.04230405 0.01908453   TFRC     1
## GO:0019834 0.0017266959 0.04230405 0.01908453  ANXA1     1
## GO:0120283 0.0030200053 0.04932675 0.02225267   XIAP     1
##                    ID                                    Description GeneRatio
## GO:0050900 GO:0050900                            leukocyte migration       4/8
## GO:0071621 GO:0071621                         granulocyte chemotaxis       3/8
## GO:0045785 GO:0045785           positive regulation of cell adhesion       4/8
## GO:0097530 GO:0097530                          granulocyte migration       3/8
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation       3/8
## GO:0002520 GO:0002520                      immune system development       3/8
##              BgRatio       pvalue    p.adjust      qvalue                geneID
## GO:0050900 396/18888 1.246268e-05 0.004831597 0.002194346 MAPK3/PREX1/RET/ANXA1
## GO:0071621 128/18888 1.660669e-05 0.004831597 0.002194346     MAPK3/PREX1/ANXA1
## GO:0045785 485/18888 2.769198e-05 0.004831597 0.002194346  PREX1/RET/TFRC/ANXA1
## GO:0097530 154/18888 2.888705e-05 0.004831597 0.002194346     MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 3.486001e-05 0.004831597 0.002194346      MAPK3/TFRC/ANXA1
## GO:0002520 197/18888 6.021118e-05 0.006808100 0.003092006        MAPK3/RET/TFRC
##            Count
## GO:0050900     4
## GO:0071621     3
## GO:0045785     4
## GO:0097530     3
## GO:0070665     3
## GO:0002520     3
##                    ID                      Description GeneRatio   BgRatio
## GO:0005769 GO:0005769                   early endosome       4/8 428/19894
## GO:0016323 GO:0016323      basolateral plasma membrane       3/8 255/19894
## GO:0009925 GO:0009925            basal plasma membrane       3/8 286/19894
## GO:0045178 GO:0045178               basal part of cell       3/8 305/19894
## GO:0016328 GO:0016328          lateral plasma membrane       2/8  68/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/8   8/19894
##                  pvalue     p.adjust       qvalue               geneID Count
## GO:0005769 1.380895e-05 0.0007180654 0.0004215363 MAPK3/RET/TFRC/ANXA1     4
## GO:0016323 1.111412e-04 0.0024536609 0.0014404082     TFRC/CLDN7/ANXA1     3
## GO:0009925 1.560820e-04 0.0024536609 0.0014404082     TFRC/CLDN7/ANXA1     3
## GO:0045178 1.887431e-04 0.0024536609 0.0014404082     TFRC/CLDN7/ANXA1     3
## GO:0016328 3.180919e-04 0.0033081558 0.0019420348          CLDN7/ANXA1     2
## GO:1990712 3.213091e-03 0.0278467858 0.0163473034                 TFRC     1
##                    ID                                             Description
## GO:0004713 GO:0004713                        protein tyrosine kinase activity
## GO:0030235 GO:0030235                nitric-oxide synthase regulator activity
## GO:0004714 GO:0004714 transmembrane receptor protein tyrosine kinase activity
## GO:0043560 GO:0043560                      insulin receptor substrate binding
## GO:0019199 GO:0019199          transmembrane receptor protein kinase activity
## GO:0071889 GO:0071889                                  14-3-3 protein binding
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0004713      4/23 138/18522 2.340073e-05 0.002777270 0.001575410
## GO:0030235      2/23   7/18522 3.085855e-05 0.002777270 0.001575410
## GO:0004714      3/23  60/18522 5.465172e-05 0.003279103 0.001860076
## GO:0043560      2/23  13/18522 1.140988e-04 0.004477197 0.002539697
## GO:0019199      3/23  79/18522 1.243666e-04 0.004477197 0.002539697
## GO:0071889      2/23  32/18522 7.152122e-04 0.021456366 0.012171155
##                         geneID Count
## GO:0004713 MET/IGF1R/PRKCD/RET     4
## GO:0030235           ESR1/AKT1     2
## GO:0004714       MET/IGF1R/RET     3
## GO:0043560         IGF1R/PRKCD     2
## GO:0019199       MET/IGF1R/RET     3
## GO:0071889           ESR1/AKT1     2
##                    ID                             Description GeneRatio
## GO:0010720 GO:0010720 positive regulation of cell development      8/23
## GO:0045785 GO:0045785    positive regulation of cell adhesion      8/23
## GO:0048872 GO:0048872          homeostasis of number of cells      7/23
## GO:0051384 GO:0051384              response to glucocorticoid      5/23
## GO:0097305 GO:0097305                     response to alcohol      6/23
## GO:0048732 GO:0048732                       gland development      7/23
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0010720 454/18888 3.742111e-08 4.945373e-05 2.099872e-05
## GO:0045785 485/18888 6.232344e-08 4.945373e-05 2.099872e-05
## GO:0048872 322/18888 7.604366e-08 4.945373e-05 2.099872e-05
## GO:0051384 134/18888 5.063281e-07 2.032025e-04 8.628255e-05
## GO:0097305 259/18888 5.207650e-07 2.032025e-04 8.628255e-05
## GO:0048732 449/18888 7.218445e-07 2.227905e-04 9.459987e-05
##                                              geneID Count
## GO:0010720 BCL2/KRAS/FOXO3/FN1/TGM2/EEF2K/RET/ANXA1     8
## GO:0045785 AKT1/FOXO3/FN1/TGM2/PREX1/RET/TFRC/ANXA1     8
## GO:0048872     G6PD/BCL2/KRAS/AKT1/FOXO3/XIAP/ANXA1     7
## GO:0051384              BCL2/IGF1R/FOXO3/TYMS/ANXA1     5
## GO:0097305         G6PD/AKT1/IGF1R/FOXO3/TYMS/CLDN7     6
## GO:0048732       ESR1/MET/BCL2/CCND1/AKT1/TGM2/TYMS     7
##                    ID                  Description GeneRatio   BgRatio
## GO:0009925 GO:0009925        basal plasma membrane      4/23 286/19894
## GO:0045178 GO:0045178           basal part of cell      4/23 305/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      3/23 219/19894
## GO:0097128 GO:0097128       cyclin D1-CDK4 complex      1/23   2/19894
## GO:0097138 GO:0097138            BAD-BCL-2 complex      1/23   2/19894
## GO:0016328 GO:0016328      lateral plasma membrane      2/23  68/19894
##                  pvalue   p.adjust     qvalue               geneID Count
## GO:0009925 0.0002985362 0.02076713 0.01443972 MET/TFRC/CLDN7/ANXA1     4
## GO:0045178 0.0003810483 0.02076713 0.01443972 MET/TFRC/CLDN7/ANXA1     4
## GO:0005741 0.0019805936 0.03692764 0.02567639      BCL2/KRAS/FOXO3     3
## GO:0097128 0.0023109764 0.03692764 0.02567639                CCND1     1
## GO:0097138 0.0023109764 0.03692764 0.02567639                 BCL2     1
## GO:0016328 0.0027805761 0.03692764 0.02567639          CLDN7/ANXA1     2
##                    ID                               Description GeneRatio
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     11/59
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     10/59
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      5/59
## GO:0051400 GO:0051400                         BH domain binding      3/59
## GO:0031625 GO:0031625          ubiquitin protein ligase binding      8/59
## GO:0044389 GO:0044389     ubiquitin-like protein ligase binding      8/59
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 2.758963e-07 8.718322e-05 4.501465e-05
## GO:0004674 427/18522 8.742183e-07 1.275162e-04 6.583946e-05
## GO:0045309  59/18522 1.210596e-06 1.275162e-04 6.583946e-05
## GO:0051400   9/18522 2.544052e-06 2.009801e-04 1.037706e-04
## GO:0031625 305/18522 5.275026e-06 3.333817e-04 1.721324e-04
## GO:0044389 324/18522 8.207994e-06 4.322877e-04 2.231998e-04
##                                                               geneID Count
## GO:0140297 MYC/VHL/BCL2/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN    11
## GO:0004674   PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK    10
## GO:0045309                                YWHAZ/MAPK3/IRS1/YWHAB/SYK     5
## GO:0051400                                          BCL2/BAK1/BCL2L1     3
## GO:0031625             CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8     8
## GO:0044389             CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8     8
##                    ID                                 Description GeneRatio
## GO:0097305 GO:0097305                         response to alcohol     17/59
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     14/59
## GO:0104004 GO:0104004 cellular response to environmental stimulus     14/59
## GO:0010332 GO:0010332                 response to gamma radiation      8/59
## GO:2001233 GO:2001233   regulation of apoptotic signaling pathway     14/59
## GO:0010212 GO:0010212              response to ionizing radiation     10/59
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0097305 259/18888 2.098797e-18 6.774918e-15 2.969246e-15
## GO:0071214 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0104004 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0010332  52/18888 3.742034e-12 3.019822e-09 1.323498e-09
## GO:2001233 396/18888 1.424590e-11 7.768814e-09 3.404841e-09
## GO:0010212 138/18888 1.444018e-11 7.768814e-09 3.404841e-09
##                                                                                                            geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/CASP8/PTCH1
## GO:0071214                      CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004                      CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0010332                                                            CDKN1A/MYC/BCL2/BAK1/TP53/YAP1/PARP1/BCL2L1
## GO:2001233                         MYC/BCL2/BAK1/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212                                                CDKN1A/MYC/BCL2/BAK1/CASP3/TP53/YAP1/PARP1/RAD51/BCL2L1
##            Count
## GO:0097305    17
## GO:0071214    14
## GO:0104004    14
## GO:0010332     8
## GO:2001233    14
## GO:0010212    10
##                    ID                  Description GeneRatio   BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex      4/59  10/19894
## GO:0005901 GO:0005901                      caveola      6/59  82/19894
## GO:0044853 GO:0044853         plasma membrane raft      6/59 113/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      7/59 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      7/59 248/19894
## GO:0019867 GO:0019867               outer membrane      7/59 250/19894
##                  pvalue     p.adjust       qvalue
## GO:0097136 1.445555e-08 3.527155e-06 1.993345e-06
## GO:0005901 1.541329e-07 1.880421e-05 1.062706e-05
## GO:0044853 1.036054e-06 8.426574e-05 4.762214e-05
## GO:0005741 3.735501e-06 2.278656e-04 1.287765e-04
## GO:0031968 8.442607e-06 3.617766e-04 2.044553e-04
## GO:0019867 8.896146e-06 3.617766e-04 2.044553e-04
##                                               geneID Count
## GO:0097136                  BCL2/BAK1/BCL2L11/BCL2L1     4
## GO:0005901      CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0044853      CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0005741 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
## GO:0031968 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
## GO:0019867 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
##                    ID                               Description GeneRatio
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     11/59
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     10/59
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      5/59
## GO:0051400 GO:0051400                         BH domain binding      3/59
## GO:0031625 GO:0031625          ubiquitin protein ligase binding      8/59
## GO:0044389 GO:0044389     ubiquitin-like protein ligase binding      8/59
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 2.758963e-07 8.718322e-05 4.501465e-05
## GO:0004674 427/18522 8.742183e-07 1.275162e-04 6.583946e-05
## GO:0045309  59/18522 1.210596e-06 1.275162e-04 6.583946e-05
## GO:0051400   9/18522 2.544052e-06 2.009801e-04 1.037706e-04
## GO:0031625 305/18522 5.275026e-06 3.333817e-04 1.721324e-04
## GO:0044389 324/18522 8.207994e-06 4.322877e-04 2.231998e-04
##                                                               geneID Count
## GO:0140297 MYC/VHL/BCL2/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN    11
## GO:0004674   PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/CDK1/EEF2K/SYK    10
## GO:0045309                                YWHAZ/MAPK3/IRS1/YWHAB/SYK     5
## GO:0051400                                          BCL2/BAK1/BCL2L1     3
## GO:0031625             CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8     8
## GO:0044389             CDKN1A/BCL2/TP53/YWHAZ/PARP1/CTNNB1/JUN/CASP8     8
##                    ID                                 Description GeneRatio
## GO:0097305 GO:0097305                         response to alcohol     17/59
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     14/59
## GO:0104004 GO:0104004 cellular response to environmental stimulus     14/59
## GO:0010332 GO:0010332                 response to gamma radiation      8/59
## GO:2001233 GO:2001233   regulation of apoptotic signaling pathway     14/59
## GO:0010212 GO:0010212              response to ionizing radiation     10/59
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0097305 259/18888 2.098797e-18 6.774918e-15 2.969246e-15
## GO:0071214 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0104004 334/18888 1.446198e-12 1.556109e-09 6.819965e-10
## GO:0010332  52/18888 3.742034e-12 3.019822e-09 1.323498e-09
## GO:2001233 396/18888 1.424590e-11 7.768814e-09 3.404841e-09
## GO:0010212 138/18888 1.444018e-11 7.768814e-09 3.404841e-09
##                                                                                                            geneID
## GO:0097305 CDKN1A/BAK1/PARP1/CTNNB1/IGF1R/TYMS/FOXO3/CLDN7/CTNNA1/EIF4G1/AKT1/RAD51/ACACA/CDK1/BCL2L1/CASP8/PTCH1
## GO:0071214                      CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0104004                      CDKN1A/MYC/BAK1/CASP3/TP53/YAP1/PARP1/IGF1R/PIK3CA/MAPK3/RAD51/CHEK1/BCL2L1/CASP8
## GO:0010332                                                            CDKN1A/MYC/BCL2/BAK1/TP53/YAP1/PARP1/BCL2L1
## GO:2001233                         MYC/BCL2/BAK1/BCL2L11/TP53/YAP1/PARP1/CTNNB1/RAF1/CTNNA1/AKT1/MAPK9/BCL2L1/RET
## GO:0010212                                                CDKN1A/MYC/BCL2/BAK1/CASP3/TP53/YAP1/PARP1/RAD51/BCL2L1
##            Count
## GO:0097305    17
## GO:0071214    14
## GO:0104004    14
## GO:0010332     8
## GO:2001233    14
## GO:0010212    10
##                    ID                  Description GeneRatio   BgRatio
## GO:0097136 GO:0097136 Bcl-2 family protein complex      4/59  10/19894
## GO:0005901 GO:0005901                      caveola      6/59  82/19894
## GO:0044853 GO:0044853         plasma membrane raft      6/59 113/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      7/59 219/19894
## GO:0031968 GO:0031968     organelle outer membrane      7/59 248/19894
## GO:0019867 GO:0019867               outer membrane      7/59 250/19894
##                  pvalue     p.adjust       qvalue
## GO:0097136 1.445555e-08 3.527155e-06 1.993345e-06
## GO:0005901 1.541329e-07 1.880421e-05 1.062706e-05
## GO:0044853 1.036054e-06 8.426574e-05 4.762214e-05
## GO:0005741 3.735501e-06 2.278656e-04 1.287765e-04
## GO:0031968 8.442607e-06 3.617766e-04 2.044553e-04
## GO:0019867 8.896146e-06 3.617766e-04 2.044553e-04
##                                               geneID Count
## GO:0097136                  BCL2/BAK1/BCL2L11/BCL2L1     4
## GO:0005901      CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0044853      CTNNB1/IGF1R/MAPK3/IRS1/CTNNA1/PTCH1     6
## GO:0005741 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
## GO:0031968 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
## GO:0019867 BCL2/BAK1/BCL2L11/RAF1/FOXO3/BCL2L1/CASP8     7
##                    ID                             Description GeneRatio
## GO:0004998 GO:0004998           transferrin receptor activity       1/6
## GO:0019834 GO:0019834     phospholipase A2 inhibitor activity       1/6
## GO:0120283 GO:0120283 protein serine/threonine kinase binding       1/6
## GO:0004859 GO:0004859        phospholipase inhibitor activity       1/6
## GO:0055102 GO:0055102               lipase inhibitor activity       1/6
## GO:0004707 GO:0004707                     MAP kinase activity       1/6
##             BgRatio       pvalue   p.adjust     qvalue geneID Count
## GO:0004998  2/18522 0.0006477907 0.02979033 0.01227062   TFRC     1
## GO:0019834  4/18522 0.0012952318 0.02979033 0.01227062  ANXA1     1
## GO:0120283  7/18522 0.0022657379 0.03302896 0.01360461   XIAP     1
## GO:0004859 11/18522 0.0035585234 0.03302896 0.01360461  ANXA1     1
## GO:0055102 15/18522 0.0048499126 0.03302896 0.01360461  ANXA1     1
## GO:0004707 16/18522 0.0051725419 0.03302896 0.01360461  MAPK3     1
##                    ID                                    Description GeneRatio
## GO:0071621 GO:0071621                         granulocyte chemotaxis       3/6
## GO:0097530 GO:0097530                          granulocyte migration       3/6
## GO:0070665 GO:0070665 positive regulation of leukocyte proliferation       3/6
## GO:0030595 GO:0030595                           leukocyte chemotaxis       3/6
## GO:0097529 GO:0097529                    myeloid leukocyte migration       3/6
## GO:0032872 GO:0032872    regulation of stress-activated MAPK cascade       2/6
##              BgRatio       pvalue    p.adjust       qvalue            geneID
## GO:0071621 128/18888 5.990226e-06 0.002463257 0.0008761002 MAPK3/PREX1/ANXA1
## GO:0097530 154/18888 1.044150e-05 0.002463257 0.0008761002 MAPK3/PREX1/ANXA1
## GO:0070665 164/18888 1.261053e-05 0.002463257 0.0008761002  MAPK3/TFRC/ANXA1
## GO:0030595 237/18888 3.794128e-05 0.004308506 0.0015323947 MAPK3/PREX1/ANXA1
## GO:0097529 239/18888 3.890475e-05 0.004308506 0.0015323947 MAPK3/PREX1/ANXA1
## GO:0032872  35/18888 4.980407e-05 0.004308506 0.0015323947       MAPK3/FOXM1
##            Count
## GO:0071621     3
## GO:0097530     3
## GO:0070665     3
## GO:0030595     3
## GO:0097529     3
## GO:0032872     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0005769 GO:0005769                   early endosome       3/6 428/19894
## GO:0016323 GO:0016323      basolateral plasma membrane       2/6 255/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/6   8/19894
## GO:0009925 GO:0009925            basal plasma membrane       2/6 286/19894
## GO:0045178 GO:0045178               basal part of cell       2/6 305/19894
## GO:0031143 GO:0031143                     pseudopodium       1/6  18/19894
##                  pvalue    p.adjust     qvalue           geneID Count
## GO:0005769 0.0001884452 0.008856923 0.00416563 MAPK3/TFRC/ANXA1     3
## GO:0016323 0.0023728661 0.031715571 0.01491662       TFRC/ANXA1     2
## GO:1990712 0.0024106661 0.031715571 0.01491662             TFRC     1
## GO:0009925 0.0029736864 0.031715571 0.01491662       TFRC/ANXA1     2
## GO:0045178 0.0033739969 0.031715571 0.01491662       TFRC/ANXA1     2
## GO:0031143 0.0054171867 0.038952261 0.01832021            MAPK3     1
##                    ID                                        Description
## GO:0004857 GO:0004857                          enzyme inhibitor activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0004860 GO:0004860                  protein kinase inhibitor activity
## GO:0004998 GO:0004998                      transferrin receptor activity
## GO:0019210 GO:0019210                          kinase inhibitor activity
## GO:0072341 GO:0072341                        modified amino acid binding
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:0004857      4/15 389/18522 0.0002176436 0.02205928 0.01245452
## GO:0030291      2/15  37/18522 0.0004010778 0.02205928 0.01245452
## GO:0004860      2/15  73/18522 0.0015562116 0.03903069 0.02203647
## GO:0004998      1/15   2/18522 0.0016190833 0.03903069 0.02203647
## GO:0019210      2/15  78/18522 0.0017741224 0.03903069 0.02203647
## GO:0072341      2/15 101/18522 0.0029515609 0.04762216 0.02688715
##                            geneID Count
## GO:0004857 CDKN1A/AKT1/XIAP/ANXA1     4
## GO:0030291            CDKN1A/AKT1     2
## GO:0004860            CDKN1A/AKT1     2
## GO:0004998                   TFRC     1
## GO:0019210            CDKN1A/AKT1     2
## GO:0072341             TYMS/ANXA1     2
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0070482 GO:0070482
## GO:0070665 GO:0070665
## GO:0051347 GO:0051347
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0070482                                       response to oxygen levels
## GO:0070665                  positive regulation of leukocyte proliferation
## GO:0051347                     positive regulation of transferase activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051054      6/15 301/18888 6.912116e-08 9.511072e-05 3.870785e-05
## GO:0032872      3/15  35/18888 2.611906e-06 1.247709e-03 5.077886e-04
## GO:0070302      3/15  38/18888 3.361733e-06 1.247709e-03 5.077886e-04
## GO:0070482      5/15 354/18888 5.784493e-06 1.247709e-03 5.077886e-04
## GO:0070665      4/15 164/18888 6.941399e-06 1.247709e-03 5.077886e-04
## GO:0051347      5/15 376/18888 7.756126e-06 1.247709e-03 5.077886e-04
##                                      geneID Count
## GO:0051054 CDKN1A/MYC/AKT1/MAPK3/FOXM1/TFRC     6
## GO:0032872                  MYC/MAPK3/FOXM1     3
## GO:0070302                  MYC/MAPK3/FOXM1     3
## GO:0070482         CDKN1A/MYC/VHL/AKT1/TFRC     5
## GO:0070665          CDKN1A/MAPK3/TFRC/ANXA1     4
## GO:0051347        CDKN1A/MYC/AKT1/MAPK3/RET     5
##                    ID                 Description GeneRatio   BgRatio
## GO:0005769 GO:0005769              early endosome      4/15 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane      3/15 255/19894
## GO:0016328 GO:0016328     lateral plasma membrane      2/15  68/19894
## GO:0009925 GO:0009925       basal plasma membrane      3/15 286/19894
## GO:0045178 GO:0045178          basal part of cell      3/15 305/19894
## GO:0070557 GO:0070557            PCNA-p21 complex      1/15   2/19894
##                  pvalue   p.adjust     qvalue               geneID Count
## GO:0005769 0.0002388682 0.01636673 0.01224104 MAPK3/RET/TFRC/ANXA1     4
## GO:0016323 0.0008449199 0.01636673 0.01224104     TFRC/CLDN7/ANXA1     3
## GO:0016328 0.0011745366 0.01636673 0.01224104          CLDN7/ANXA1     2
## GO:0009925 0.0011769074 0.01636673 0.01224104     TFRC/CLDN7/ANXA1     3
## GO:0045178 0.0014160699 0.01636673 0.01224104     TFRC/CLDN7/ANXA1     3
## GO:0070557 0.0015074617 0.01636673 0.01224104               CDKN1A     1
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
## Warning: ggrepel: 17 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
## Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

#goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_glmnet_cox.rds")